Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data

Staklinski, Stephen J, Scheben, Armin, Brault, Lise M, Hassett, Rebecca, Serio, Ryan N, Xing, Jiawei, Nowak, Dawid G, Siepel, Adam (June 2026) Bayesian inference of tissue-migration histories in metastatic cancer from cell-lineage tracing data. Cell Genomics, 6 (6). p. 101193. ISSN 2666-979X

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Abstract

Cell-lineage tracing now enables direct study of tissue migration in metastatic cancer, but current reconstruction algorithms are limited by a reliance on strong parsimony assumptions and pre-estimated cell-lineage phylogenies. Here, we introduce a probabilistic modeling and inference framework, called Bayesian Evolutionary Analysis of Metastasis (BEAM), which provides richer information about complex metastatic histories. Based on the flexible BEAST 2 platform for Bayesian phylogenetics, BEAM infers a full posterior distribution over cell-lineage phylogenies and tissue-migration graphs, complete with timing information. We show using simulated data that BEAM reliably outperforms current methods for inference of tissue-migration graphs, especially for more complex histories. We then apply BEAM to public datasets for lung and prostate cancer, finding support for distinct modes of migration across clones and reseeding of primary tumors. Overall, BEAM serves as a powerful framework for revealing the modes, timing, and directionality of tissue migration in metastatic cancer.

Item Type: Paper
Subjects: diseases & disorders > cancer
diseases & disorders
diseases & disorders > cancer > metastasis
CSHL Authors:
Communities: CSHL labs > Siepel lab
CSHL Post Doctoral Fellows
School of Biological Sciences > Publications
SWORD Depositor: CSHL Elements
Depositing User: CSHL Elements
Date: 10 June 2026
Date Deposited: 17 Jun 2026 11:37
Last Modified: 17 Jun 2026 11:37
PMCID: PMC13261679
Related URLs:
URI: https://repository.cshl.edu/id/eprint/42225

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